From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH 1/3] gnu: Add python-screed. Date: Fri, 17 Jun 2016 11:23:19 +1000 Message-ID: <1466126601-30932-2-git-send-email-donttrustben@gmail.com> References: <1466126601-30932-1-git-send-email-donttrustben@gmail.com> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:55664) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bDiVb-00080g-5n for Guix-devel@gnu.org; Thu, 16 Jun 2016 21:23:47 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bDiVV-0000uV-Ij for Guix-devel@gnu.org; Thu, 16 Jun 2016 21:23:42 -0400 Received: from mail-pa0-x235.google.com ([2607:f8b0:400e:c03::235]:36576) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bDiVV-0000uR-Bb for Guix-devel@gnu.org; Thu, 16 Jun 2016 21:23:37 -0400 Received: by mail-pa0-x235.google.com with SMTP id b5so23095857pas.3 for ; Thu, 16 Jun 2016 18:23:37 -0700 (PDT) Received: from localhost.localdomain ([103.25.181.216]) by smtp.googlemail.com with ESMTPSA id pk18sm32320490pab.27.2016.06.16.18.23.33 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-SHA bits=128/128); Thu, 16 Jun 2016 18:23:35 -0700 (PDT) In-Reply-To: <1466126601-30932-1-git-send-email-donttrustben@gmail.com> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Guix-devel@gnu.org * gnu/packages/bioinformatics.scm (python-screed, python2-screed): New variables. --- gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 04ed769..22ed71a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3359,6 +3359,47 @@ optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.") (license license:gpl3+))) +(define-public python-screed + (package + (name "python-screed") + (version "0.9") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/a0/6b/" + "a90c7ab7b0ad1eab211053c85c1242a81379f34c5f5933392079c9b36858" + "/screed-" version ".tar.gz")) + (sha256 + (base32 + "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "PYTHONPATH" + (string-append (getenv "PYTHONPATH") ":.")) + (zero? (system* "nosetests" "--attr" "!known_failing"))))))) + (native-inputs + `(("python-nose" ,python-nose))) + (inputs + `(("python-bz2file" ,python-bz2file))) + (home-page "http://github.com/dib-lab/screed/") + (synopsis "Short read sequence utils") + (description "Screed parses FASTA and FASTQ files and generates databases. +Values such as sequence name, sequence description, sequence quality and the +sequence itself can be retrieved from these databases.") + (license license:bsd-3))) + +(define-public python2-screed + (let ((base (package-with-python2 (strip-python2-variant python-screed)))) + (package + (inherit base) + (native-inputs `(("python2-setuptools" ,python2-setuptools) + ,@(package-native-inputs base)))))) + (define-public sra-tools (package (name "sra-tools") -- 2.7.4